Heavy metal pollution is a worldwide environmental and human health problem. Prosopis laevigata is a hyperaccumulator legume that bioaccumulates Pb, Cu and Zn. With interest in designing phytoremediation strategies for sites contaminated with heavy metals, we isolated and characterized endophytic fungi from the roots of P. laevigata growing on mine tailings located in Morelos, Mexico. Ten endophytic isolates were selected by morphological discrimination and a preliminary minimum inhibitory concentration was determined for zinc, lead and copper. A novel strain of Aspergillus closest to Aspergillus luchuensis was determined to be a metallophile and presented a marked tolerance to high concentrations of Cu, Zn and Pb, so it was further investigated for removal of metals and promotion of plant growth under greenhouse conditions. The control substrate with fungi promoted larger size characters in P. laevigata individuals in comparison with the other treatments, demonstrating that A. luchuensis strain C7 is a growth-promoting agent for P. laevigata individuals. The fungus favors the translocation of metals from roots to leaves in P. laevigata, promoting an increased Cu translocation. This new A. luchuensis strain showed endophytic character and plant growth-promotion activity, high metal tolerance, and an ability to increase copper translocation. We propose it as a novel, effective and sustainable bioremediation strategy for copper-polluted soils.